Activated Carbon will really help make that water look crystal clear. That is what I run.

You could also run a very fine micron filter on the intake of your overflow or similar area where water flows through. This will catch all the fine particulates that are in the water. However, you will need to clean it often.

Wher would I put the carbon and what would I put it in? I use an Aquafuge pro from CPR its split into 3 chambers, intake side with the skimmer, middle is the refuge, and the third is the sump(very small if you ask me) which my mag 18 sits in and takes up alot of room. As for the micron bag would it still work if it was completely submerged in water where my overflow enters my Aquafuge?

The carbon simply needs to be in a high flow area. You can put it in a media bag which can be purchased at the LFS. Some people use pantyhose or cheese cloth as well, but for the price of the media bag (~$2) I just buy those.

My carbon sits right under the output of my overflow in the bottom of my sump. That way every bit of water that passes through the tank, at some point, comes in contact with the carbon. You will need to determine the best place to put the carbon.

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As for the micron bag would it still work if it was completely submerged in water where my overflow enters my Aquafuge?

I have found that filters tend to work better when water is being drawn into them rather than being pushed through them (make sense?). In other words, you could try to put the micron sock over the overflow inlet so as water goes into the overflow, it passes through the sock.